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Title: EST-PCR Markers Representing Watermelon Fruit Genes are Polymorphic among Watermelon Heirloom Cultivars Sharing a Narrow Genetic Base

Author
item Levi, Amnon
item Wechter, William - Pat
item Davis, Angela

Submitted to: Plant Genetic Resources
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/24/2008
Publication Date: 4/15/2009
Citation: Levi, A., Wechter, W.P., Davis, A.R. 2009. EST-PCR Markers Representing Watermelon Fruit Genes are Polymorphic among Watermelon Heirloom Cultivars Sharing a Narrow Genetic Base. Plant Genetic Resources. 7:16-32.

Interpretive Summary: Watermelon is an important crop in the USA, with a farm value of $300 million. In recent years, there is great interest by consumer groups and the watermelon industry to improve the nutritional quality of watermelon. Consumers and plant breeders have particular interest in enhancing the content of antioxidant compounds called ‘carotenoids’ and ‘flavonoids’ in watermelon. These compounds are considered to be important dietary components in maintaining health and in preventing cancer and heart disease. Developing watermelon cultivars with enhanced nutritional quality will benefit consumer health. In this study, we used biotechnology tools to isolate genes from watermelon fruit, and identified a set of 140 genes that control watermelon fruit quality. We determined that these genes varied in their DNA sequences in different types of watermelon. These differences in DNA sequence allowed us to develop DNA markers useful in genetic studies of watermelon. The information provided in this study can be useful for the watermelon research industry and watermelon breeders using DNA markers aimed at enhancing watermelon fruit quality and nutritional value.

Technical Abstract: To date there are only a few sequenced-tagged site (STS) markers associated with genes controlling fruit quality in watermelon. In this study, we examined polymorphism in coding regions of genes expressed in watermelon fruit. A normalized cDNA library was constructed for watermelon fruit (Citrullus lanatus var. lanatus) and 4,700 non-redundant expressed sequence tags (EST-unigenes) associated with watermelon fruit development were constructed (http://www.icugi.org). Forty ESTs containing simple sequence repeat (SSR) motives (EST-SSRs) and sixty ESTs differentially expressed in watermelon fruit were used for designing primer for PCR. The EST primer pairs were tested in PCR amplification with genomic DNA of 25 watermelon heirloom cultivars and 13 United States Plant Introductions (U.S. PIs) of Citrullus sp., including 4 Citrullus lanatus var. lanatus, 5 Citrullus lanatus var. citroides PIs, and 4 Citrullus colocynthis PIs. The 40 EST-SSR and 60 EST primer pairs produced 108 EST-SSR and 142 EST-PCR markers, respectively, among the Citrullus PIs and watermelon cultivars. A large number of EST-SSR and EST-PCR markers were found in Citrullus PIs, but not in any of the watermelon cultivars. Of the 108 EST-SSR markers, 103 exist in Citrullus PIs and 64 in the cultivars. Of these 64 EST-SSR markers associated with the cultivars, 45 were found to be polymorphic. Of the 142 EST-PCR markers, 133 exist in the Citrullus PIs and 108 in the cultivars. Of these 108 EST-PCR markers, 85 are polymorphic among cultivars. The results in this study indicate that polymorphism exist in many of the coding regions of watermelon fruit. In total, 130 polymorphic EST-markers (45 EST-SSR and 85 EST-PCR markers) associated with watermelon fruit were generated using the above data. These markers should be useful for DNA fingerprinting of cultivars and breeding lines, and in genetic mapping of the watermelon genome.